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Data Flow

Information about Laue symmetry or lattice centering. SMART. SADABS. SAINT. copy to sad.p4p. XPREP. SHELX. Editor or XP. Data Flow. 04000-n.xxx 04000-1.p4p. 04000-n.raw 04000-n._ls 04000-m.p4p. sad.hkl sad.abs. sad.prp name.ins name.hkl. name.ins. name.res

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Data Flow

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  1. Information about Laue symmetry or lattice centering SMART SADABS SAINT copy to sad.p4p XPREP SHELX Editor or XP Data Flow 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p sad.hkl sad.abs sad.prp name.ins name.hkl name.ins name.res name.lst

  2. Information about Laue symmetry or lattice centering SADABS SAINT copy to sad.p4p SHELX Editor or XP Data Flow SMART 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p sad.hkl sad.abs XPREP sad.prp name.ins name.hkl name.ins name.res name.lst

  3. copy to sad.p4p SHELX Editor or XP Data Flow SMART Information about Laue symmetry or lattice centering 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p SAINT SADABS sad.hkl sad.abs XPREP sad.prp name.ins name.hkl name.ins name.res name.lst

  4. SMART SADABS XPREP SAINT copy to sad.p4p SHELX Editor or XP Data Flow Information about Laue symmetry or lattice centering 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p sad.hkl sad.abs sad.prp name.ins name.hkl name.ins name.res name.lst

  5. SMART SADABS XPREP SAINT copy to sad.p4p SHELX Editor or XP Data Flow Information about Laue symmetry or lattice centering 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p sad.hkl sad.abs sad.prp name.ins name.hkl name.ins name.res name.lst

  6. SHELX Editor or XP Data Flow name.hkl name.ins name.lst name.fcf name.cif name.pdb etc. name.res

  7. XCIF SHELX Editor or XP Ray tracer Data Flow name.hkl name.ins name.lst name.fcf name.cif name.pdb etc. name.res name.rtf name.bmp Paper / Grant proposal

  8. Structure Solution with SHELXS SHELXS is a very automatic Black Box. PATT solves a Patterson and is best for structures with a few heavy atoms in combination with many light atoms. Works very good in centrosymmetric space groups. TREF uses direct methods. You need atomic resolution (say 1.2 Å or better). Read: Sheldrick, G. M. Acta Cryst. Sect. A (1990), 46, 467. Direct methods have problems in the presence of inversion centers (use PATT or solve in non-centrosymmetric space group and transform by hand). Sometimes TREF 1000 (or 5000) helps.

  9. Structure Refinement The solution from SHELXS is frequently already very good. However, the coordinates are not quite accurate, the atom types of some or all atoms have been assigned incorrectly (if at all), and details of the structure are missing (H-atoms, disorders, solvent molecules, etc.). The atomic positions in the first . res file are not the direct result of the diffraction experiment, but an interpretation of the electron density function calculated from the measured intensities and the “somehow determined” phase angles. Better phases can be calculated from the atomic positions, which allow re-determining of the electron density function with a higher precision. From the new electron density map, more accurate atomic positions can be derived, which lead to even better phase angles, and so forth.

  10. Structure Refinement Close examination of the Fo-Fc map helps to introduce new atoms and remove “bad” old ones. Once all non-hydrogen atoms are found, the atoms can be refined anisotropically. Once the model is anisotropic, the hydrogen atom positions can be determined or calculated.

  11. Evalution of the Model The model should only be altered if a change improves its quality. How to judge quality of the model? Least-squares approach: By means of Fourier transformation, a complete set of structure factors is calculated from the atomic model. The calculated intensities are then compared with the measured intensities, and the best model is that, which gives the smallest value for the minimization function M. or F: structure factor; o: observed; c: calculated; w weighting factor (derived from σ).

  12. or F: structure factor; o: observed; c: calculated; w weighting factor (derived from σ). Refinement against F2 or F? Past: F Advantage: Faster computing. Problems: I ~ F2. That means extraction of a root! Difficult for very weak reflections. Negative reflections need to be ignored or arbitrarily set to a small positive number. Estimation of σ(F) from σ(F2) is very difficult. The least squares method is very sensitive to the weights, which are calculated from the standard uncertainties. Refinement against F results in inaccuracies in the refinement. Now: F2 Advantages: none of the problems mentioned arise. Disadvantage: A little slower.

  13. Residual Values: the R factors wR2: Most closely related to refinement against F2. R1: Most popular one, based on F. GooF: S is supposed to be > 1.0 F: structure factor; o: observed; c: calculated; w weighting factor (derived from σ). NR: number of independent reflections; NP: number of refined parameters.

  14. Parameters For every atom: x, y, z coordinates and one (isotropic) or six (anisotropic) displacement parameters. For every structure: overall scale factor osf (first FVAR). Possibly additional scale factors (BASF, EXTI, SWAT, etc.). Possibly a Flack-x-parameter. Atom types are also parameters, even thought they are not refined. Incorrectly assigned atom types can cause quite some trouble. Altogether: The number of parameters is roughly ten times the number of independent atoms in a structure. For a stable refinement: data-to-parameter-ratio should be > 8 for non-centrosymmetric structures and > 10 for centrosymmetric structures.  ca. 0.84 Å or 2Θ = 50° (Mo).

  15. Constraints and Restraints Both improve the data-to-parameter-ratio: Constraints remove parameters, restraints add data.

  16. Constraints Constraints are mathematical equations, relating two or more parameters or assigning fixed numerical values to certain parameters, hence reducing the number of independent parameters to be refined. Site occupation factors are constraints present in every structure. Even for disordered atoms the sum of the occupancies is constrained to add up to 1.0. Atoms on special position require constraints for their coordinates, occupancies and sometimes also their ADPs:

  17. Special Position Constraints

  18. Special Position Constraints

  19. Special Position Constraints An atom on a twofold axis along b. A 180° rotation must not change the position of the atom or the shape of the thermal ellipsoid. From the first condition follows: (x, y, z) = (-x, y, -z), which is only true for x = z = 0. The second condition dictates: (U11, U22, U33, U23, U13, U12) = (U11, U22, U33, -U23, U13, -U12), which is only true for U23 = U12 = 0. No good Good SHELXL generates special positions automatically. Big relief.

  20. Rigid Group Constraints A group of atoms with known (or assumed) geometry: Refine six parameters (translation and rotation) rather than 3N parameters for the individual atoms (9N for anisotropic). A seventh parameter can be refined as scale factor. Typical examples: Cp or Cp* ligands, phenyl rings, SO4-, perchlorate ions, etc. In SHELXL: AFIX mn / AFIX 0 command m describes the geometry of the group and n the mathematical treatment.

  21. Hydrogen Atoms Only 1 delocalized electron. Hydrogen atoms can be “placed on mathematically calculated positions and refined using a riding model”. That means X-H distances and H-X-H or H-X-Y angles are constraint to certain values. Not the hydrogen positions! In SHELXL: HFIX mn generates the appropriate AFIX commands Again m describes the geometry of the group and n the mathematical treatment.

  22. Other Constraints EADP atom1 atom2 Forces the two atoms to have identical ADPs EXYZ atom1 atom2 Force the two atoms to have identical oordinates. EADPand EXYZ can be useful for disorders or the refinement of mixed crystals (e.g. zeolithes).

  23. Next Meeting Tuesday January 10, 2005,11:15 a.m. MOORE room (here)

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